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Updated: Jul 17, 2025
Yeast As a Chassis for Developing Functional Assays to Study Human P53
Published on: August 4, 2019
ChIP-chip data for identifying target genes and consensus binding sequences of mutant p53 in MDA-MB-468 breast cancer
Mai Nhu Uyen Le1, Yichong Ning1,2, Jianlin Zhou1
1State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, China.
Abstract:
The tumor suppressor p53 exerts its role mainly as a transcription factor. The TP53 gene, which encodes the p53 protein, is the most commonly mutated gene in human cancers, particularly triple negative breast cancer (TNBC). Variations in the TP53 gene occur mainly in exons 5-8 and result in missense mutations in the DNA-binding domain of the p53 protein that alter DNA binding specificity. To identify the target genes of mutant p53, we performed chromatin immunoprecipitation followed by DNA microarray (ChIP-chip). Briefly, the TNBC cell line MDA-MB-468 containing the endogenous p53-R273H mutation (the arginine residue at position 273 is mutated to a histidine) was cross-linked with 1% formaldehyde and ultrasonically sheared to generate chromatin fragments in a range of 200∼1000 bp. An aliquot of the sheared chromatin was kept as input, and the other chromatin was precipitated with a p53 monoclonal antibody. DNA was purified from the precipitated chromatin and the unprecipitated chromatin (i.e., input), amplified, and labeled with Cy5 (ChIP DNA) or Cy3 (input DNA). Cy5- and Cy3-labeled DNA samples were cohybridized with the NimbleGen Human ChIP-chip 2.1 M Deluxe Promoter Array. The raw and analyzed data are described in this article. They are useful for identifying target genes and consensus binding motifs of the p53 R273H mutant and for further clarifying the molecular mechanism underlying the oncogenic activity of the p53 mutant.
Insights
Mutant p53, common in triple-negative breast cancer (TNBC), alters gene targets. This study used ChIP-chip to identify genes regulated by the p53 R273H mutation, aiding understanding of its oncogenic role.
Area of Science:
- Molecular Biology
- Cancer Genetics
- Genomics
Background:
- The TP53 gene, encoding the tumor suppressor p53 protein, is frequently mutated in human cancers, especially triple-negative breast cancer (TNBC).
- TP53 mutations, often missense mutations in exons 5-8, affect the DNA-binding domain, altering p53's target gene specificity.
- Understanding the target genes of mutant p53 is crucial for elucidating its oncogenic mechanisms.
Purpose of the Study:
- To identify target genes regulated by the common p53 R273H mutant.
- To characterize the DNA-binding motifs of the p53 R273H mutant.
- To provide data for further investigation into the molecular mechanisms of mutant p53's oncogenic activity.
Main Methods:
- Chromatin immunoprecipitation followed by DNA microarray (ChIP-chip) was employed.
- The TNBC cell line MDA-MB-468 with endogenous p53-R273H mutation was used.
- p53-bound DNA was identified using a p53 monoclonal antibody and cohybridized with a promoter array.
Main Results:
- ChIP-chip analysis identified specific DNA regions bound by the p53 R273H mutant.
- The study generated data on target genes and consensus binding motifs for the p53 R273H mutant.
- Raw and analyzed data are available for further research.
Conclusions:
- The identified target genes and binding motifs provide insights into the function of mutant p53.
- This research contributes to understanding the molecular basis of p53-driven oncogenesis in TNBC.
- The data facilitates further studies on the oncogenic activity of mutant p53.
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